Influence of loop size on the stability of intramolecular DNA quadruplexes

Nucleic Acids Research

Volumn 32, Issue 8, 2004, Pages 2598-2606

  Risitano, Antonina ^a,b   Fox, Keith R ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ETHYLENE GLYCOL; LITHIUM; OLIGONUCLEOTIDE; POTASSIUM; PROPYLENE GLYCOL; SODIUM; DNA; GUANINE; QUADRUPLEX DNA;

ARTICLE; CIRCULAR DICHROISM; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DNA DENATURATION; DNA SEQUENCE; DNA STRUCTURE; GENETIC STABILITY; HEATING; HYSTERESIS; PRIORITY JOURNAL; TELOMERE; CHEMISTRY; CONFORMATION; SPECTROFLUOROMETRY;

CIRCULAR DICHROISM; DNA; GUANINE; NUCLEIC ACID CONFORMATION; SPECTROMETRY, FLUORESCENCE;

EID: 3042671689     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh598     Document Type: Article

References (49)

1. Williamson,J.R. (1994) G-quartet structures on telomeric DNA. Annu. Rev. Biophys. Biomol. Struct., 23, 703-730.
2. Venczel,E.A. and Sen,S. (1996) Synapsable DNA. J. Mol. Biol., 257, 219-224.
3. Simonsson,T. (2001) G-quadruplex DNA structures - variations on a theme. Biol. Chem., 382, 621-628.
4. Keniry,M.A. (2000) Quadruplex structures in nucleic acids. Biopolymers, 56, 123-146.
5. Sen,D. and Gilbert,W. (1988) Formation of parallel four-stranded complexes by guanine rich motifs in DNA and its implications for meiosis. Nature, 334, 364-366.
6. Laughlan,G., Murchie,A.I.H., Norman,D.G., Moore,M.H., Moody,P.C., Lilley,D.M.J. and Luisi,B. (1994) The high-resolution crystal structure of a parallel stranded guanine tetraplex. Science, 265, 520-524.
7. Phillips,K., Dauter,Z., Murchie,A.I., Lilley,D.M.J. and Luisi,B. (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Angstrom resolution. J. Mol. Biol., 273, 171-182.
8. Sundquist,W.I. and Klug,A. (1989) Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature, 342, 825-829.
9. 2. Eur. J. Biochem., 233, 631-643.
10. Henderson,E., Hardin,C.C., Walk,S.K., Tinoco,I. and Blackburn,E.H. (1987) Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell, 51, 899-908.
11. Macaya,R.F., Schultze,P., Smith,F.W., Roe,J.A. and Feigon,J. (1993) Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc. Natl Acad. Sci. USA, 90, 3745-3749.
12. 3] G-tetraplex. Structure, 1, 76-94.
13. Parkinson,G.N., Lee,M.P.H. and Neidle,S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417, 876-880.
14. 3] G-tetraplex. J. Mol. Biol., 251, 263-282.
15. Williamson,J.R., Raghuraman,M.K. and Cech,T.R. (1989) Monovalent cation induced structure of telomeric DNA - the G-quartet model. Cell, 59, 871-880.
16. Sen,D. and Gilbert,W. (1990) A sodium-potassium switch in the formation of 4-stranded G4-DNA. Nature, 344, 410-414.
17. Guschlabauer,W., Chantot,J.F. and Thiele,D. (1990) Four stranded nucleic acid structures 25 years later: from guanosine gels to telomere DNA. J. Biomol. Struct. Dynam., 8, 491-511.
18. Sen,D. and Gilbert,W. (1992) Guanine quartet structures. Methods Enzymol., 211, 191-199.
19. Blackburn,E.H. (1991) Structure and function of telomeres. Nature, 350, 569-573.
20. Rhodes,D. and Giraldo,R. (1995) Telomere structure and function. Curr. Opin. Struct. Biol., 5, 311-322.
21. Wellinger,R.J. and Sen,D. (1997) The DNA structures at the ends of eukaryotic chromosomes Eur. J. Cancer, 33, 735-749.
22. Schaffitzel,C., Berger,I., Postberg,J. Hanes,J., Lipps,H.J. and Plückthun,A. (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonchia lemnae macronuclei. Proc. Natl Acad. Sci. USA, 98, 8572-8577.
23. Simonsson,T., Pecinka,P. and Kubista,M. (1998) DNA tetraplex formation in the control regions of c-myc. Nucleic Acids Res., 26, 1167-1172.
24. Siddiqui-Jain,A., Grand,C.L., Bearss,D.J. and Hurley,L.H. (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl Acad. Sci. USA, 99, 11593-11598.
25. Catasti,P., Chen,X., Moyzis,R.K., Bradbury,E.M. and Gupta,G. (1996) Structure-function correlations of the insulin-linked polymorphic region. J. Mol. Biol., 264, 534-545.
26. Darnell,J.C., Jensen,K.B., Jin,P., Brown,V., Warren,S.T. and Darnell,R.B. (2001) Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell, 107, 489-499.
27. Sundquist,W.I. and Heaphy,S. (1993) Evidence for interstrand quadruplex formation in the dimerization of immunodeficiency virus-1 genomic RNA. Proc. Natl Acad. Sci. USA. 90, 3393-3397.
28. Schultze,P., Macaya,R.F. and Feigon,J. (1993) Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. J. Mol. Biol., 235, 1532-1547.
29. Smirnov,I. and Shafer,R.H. (2000) Effect of loop sequence and size on DNA aptamer stability. Biochemistry, 39, 1462-1468.
30. Jing,N., Rando,R.F., Pommier,Y. and Hogan,M.E. (1997) Ion selective folding of loop domains in a potent anti-HIV oligonucleotide. Biochemistry, 36, 12498-12505.
31. Jing,N. and Hogan,M.E. (1998) Structure-activity of tetrad forming oligonucleotides as a potential anti-HIV integrase therapeutic drug. J. Biol. Chem., 273, 34992-34999.
32. Jing,N., Marchand,C., Liu,J., Mitra,R., Hogan,M.E. and Pommier,Y. (2000) Mechanism of inhibition of HIV-1 integrase by G-tetrad forming oligonucleotides in vitro. J. Biol. Chem., 275, 21460-21467.
33. Ueyama,H., Takagi,M. and Takenaka,S. (2002) A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with guanine quartet-potassium ion complex formation. J. Am. Chem. Soc., 124, 14286-14287.
34. Calzolari,A., Di Felice,R., Molinari,E. and Garbesi,A. (2002) G-quartet biomolecular nanowires. Appl. Phys. Lett., 80, 3331-3333.
35. Haider,S., Parkinson,G.N. and Neidle,S. (2002) Crystal structure of the potassium form of the Oxytricha nova G-quadruplex. J. Mol. Biol., 320, 189-200.
36. Èrnugelj,M., Šket,P. and Plvec,J. (2003) Small change in a G-rich sequence, a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations. J. Am. Chem. Soc., 125, 7866-7871.
37. 4 G-tetraplex. Structure, 2, 1141-1156.
38. Wyatt,J.R., Davis,P.W. and Freier,S.M. (1996) Kinetics of G-quartet mediated tetramer formation. Biochemistry, 35, 8002-8008.
39. Risitano,A. and Fox,K.R. (2003) Stability of intramolecular DNA quadruplexes: comparison with DNA duplexes. Biochemistry, 42, 6507-6513.
40. Darby,R.A.J., Sollogoub,M., McKeen,C., Brown,L., Risitano,A., Brown,N., Barton,C., Brown,T. and Fox,K.R. (2002) High throughput measurement of duplex, triplex and quadruplex melting curves using molecular beacons and a LightCycler. Nucleic Acids Res., 30, e39.
41. Simonsson,T. and Sjöback,R. (1999) DNA tetraplex formation studied with fluorescence resonance energy transfer. J. Biol. Chem., 274, 17379-17383.
42. Mergny,J.-L., Lacroix,L., Teulade-Fichou,M.-P., Hounsou,C., Guittat,L., Moarau,M., Arimondo,P.B., Vigneron,J.-P., Lehn,J.-M., Riou,J.F., Garestier,T. and Hélène,C. (2001) Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay. Proc. Natl Acad. Sci. USA, 98, 3062-3067.
43. 4T. Biochemistry, 31, 2455-2459.
44. Balagurumoorthy,P., Brahmachari,S.K. Mohanty,D., Bansal,M. and Sasisekharan,V. (1992) Hairpin and parallel quartet structures for telomeric sequences. Nucleic Acids Res., 20, 4061-4067.
45. Balagurumoorthy,P. and Brahmachari,S.K. (1994) Structure and stability of human telomeric sequence. J. Biol. Chem., 269, 21858-21869.
46. Lu,M., Guo,Q. and Kallenbach,N.R. (1993) Thermodynamics of G-tetraplex formation by telomeric DNAs. Biochemistry, 32, 598-601.
47. Cantor,C.R. and Schimmel,P.R. (1980) Biophysical Chemistry. W.H.Freedman and Company, New York.
48. Dapić,V., Bates,P.J. Trent,J.O., Rodger,A., Thomas,S.D. and Miller,D.M. (2002) Antiproliferative activity of G-quartet-forming oligonucleotides with backbone and sugar modifications. Biochemistry, 41, 3676-3685.
49. Dapić,V., Abdomerović,V., Marrington,R., Peberdy,J., Rodger,A., Trent,J.O. and Bates,P.J. (2003) Biophysical and biological properties of quadruplex oligdeoxyribonucleotides. Nucleic Acids Res., 31, 2097-2107.